Alignments for a candidate for glnA in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Pseudomonas fluorescens FW300-N2C3

Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase III; GSIII (uncharacterized)
to candidate AO356_30085 AO356_30085 glutamine synthetase

Query= curated2:P31592
         (435 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_30085
          Length = 444

 Score =  278 bits (711), Expect = 2e-79
 Identities = 158/424 (37%), Positives = 230/424 (54%), Gaps = 11/424 (2%)

Query: 14  IKYFMISYTDLFGGQRAKLVPAEAIADMQKDGAGFAGFA-TWLDLTPAHPDLFAVPDASS 72
           IKY +  + D+ G  + K VP   +  + ++GAGFAGFA + + + P  PD  A  D S+
Sbjct: 15  IKYVLAQFVDIHGAAKTKSVPICGLKTVAEEGAGFAGFAISGMGMEPHGPDFMARGDLST 74

Query: 73  VIQLPWKKDVAWVAADCVMDDRPVEQAPRVVLKRLVAEAAKEGLRVKTGVEPEFFLISAD 132
           +  +PW+     V     +D +P     R VL + V   A++G  + TG+EPEF L+  D
Sbjct: 75  LTPVPWQPGYGRVVCVGHVDGKPHPYDSRYVLGQQVQRLAEKGWTLNTGLEPEFNLMRRD 134

Query: 133 GS---VISDQFDTAEKPCYDQQAVMRRYDVIAEICDYMLELGWKPYQNDHEDANGQFEMN 189
            S    + D  D  +KPCYD + + R    +  + + +  + ++ YQ DHEDANGQFE+N
Sbjct: 135 ESGKLQLVDPSDNLDKPCYDYKGLSRSRVFLERLTEALQAVDFEVYQIDHEDANGQFEIN 194

Query: 190 WEYDDVLKTADKHSFFKFMVKSVAEKHGLRATFMPKPFKGLTGNGCHAHISVWDVDGRVN 249
           + Y D + +AD+ +FF+     +A   G+  +FMPKP     GNG H H+S+   D + N
Sbjct: 195 YTYSDAMTSADRFTFFRMAAGEIANDLGMICSFMPKPDPKRAGNGMHFHLSISSADNK-N 253

Query: 250 AFADKE--MAFGLSAQGKTFLGGIMKHAPALAAITNPTVNSYKRINAPRTTSGATWSPNT 307
            F D       GLS     F  G++ H PAL A   PTVNSYKR+    + SGATW+P  
Sbjct: 254 LFHDASDPSGMGLSKLAYHFAAGLLAHGPALCAFAAPTVNSYKRLVVGNSLSGATWAPAF 313

Query: 308 VTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLEGIRSQADPGQHYDIDM 367
           + +  NNR+ MVRVP  GR E RLPD   NPYL+ A IIAAGL+GI  Q +     + ++
Sbjct: 314 IAFGANNRSAMVRVP-YGRLEFRLPDAGCNPYLVSAAIIAAGLDGIDRQLEIDHVCNENL 372

Query: 368 YA---EGHLVKDAPRLPLNLLDALRAFDADEGLKAAIGAEFSSAYLKLKHLEWNAYCSHF 424
           Y+   E    +    LP +L +A  A +AD      +G +    ++KLK +EW  Y  H 
Sbjct: 373 YSLSLEQIAARGIKTLPQSLKEACDALEADPLFAEMLGPQIVDEFIKLKRMEWVEYSRHV 432

Query: 425 TQWE 428
           + WE
Sbjct: 433 SDWE 436


Lambda     K      H
   0.320    0.135    0.421 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 520
Number of extensions: 23
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 435
Length of database: 444
Length adjustment: 32
Effective length of query: 403
Effective length of database: 412
Effective search space:   166036
Effective search space used:   166036
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate AO356_30085 AO356_30085 (glutamine synthetase)
to HMM TIGR03105 (glnT: glutamine synthetase, type III (EC 6.3.1.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR03105.hmm
# target sequence database:        /tmp/gapView.23522.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03105  [M=435]
Accession:   TIGR03105
Description: gln_synth_III: glutamine synthetase, type III
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   3.6e-202  657.5   0.0   4.1e-202  657.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_30085  AO356_30085 glutamine synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_30085  AO356_30085 glutamine synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  657.3   0.0  4.1e-202  4.1e-202       2     434 ..       7     441 ..       6     442 .. 0.99

  Alignments for each domain:
  == domain 1  score: 657.3 bits;  conditional E-value: 4.1e-202
                                       TIGR03105   2 kklleekgvkyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllav 64 
                                                     +++++++g+kyvla+fvd++G+ak+k+vP+  l+++a+egagfaGfa+sg+g+eP+ +d++a 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_30085   7 QRIIDKHGIKYVLAQFVDIHGAAKTKSVPICGLKTVAEEGAGFAGFAISGMGMEPHGPDFMAR 69 
                                                     678999********************************************************* PP

                                       TIGR03105  65 pdldsliqlPwkpevawvaadlvvegkpvelapRvvlkkllaeaaekgftlktGveceffllr 127
                                                     +dl++l+++Pw+p++++v++ ++v+gkp+++++R+vl ++++++aekg+tl+tG+e+ef l+r
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_30085  70 GDLSTLTPVPWQPGYGRVVCVGHVDGKPHPYDSRYVLGQQVQRLAEKGWTLNTGLEPEFNLMR 132
                                                     *************************************************************** PP

                                       TIGR03105 128 reedgklsvaDkaDklakpcYDqralmrrydvleeisealnelGwdlYqiDheDanGqfelnf 190
                                                     r+e gkl+++D +D+l+kpcYD+++l+r++ +le+++eal+++ +++YqiDheDanGqfe+n+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_30085 133 RDESGKLQLVDPSDNLDKPCYDYKGLSRSRVFLERLTEALQAVDFEVYQIDHEDANGQFEINY 195
                                                     *************************************************************** PP

                                       TIGR03105 191 eyaDalttaDrvaffkylvkeiaeeegllatfmPkPfadrtGnGlhlhlslldedgknlfadd 253
                                                     +y+Da+t+aDr++ff++++ eia++ g++++fmPkP+ +r+GnG+h+hls+ ++d knlf+d+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_30085 196 TYSDAMTSADRFTFFRMAAGEIANDLGMICSFMPKPDPKRAGNGMHFHLSISSADNKNLFHDA 258
                                                     *************************************************************** PP

                                       TIGR03105 254 adeeglglsklayhfiaGilkhakaLaallaPtvnsYkRlvakrtlsgatWaPalisyggnnR 316
                                                     +d++g+glsklayhf aG+l+h++aL+a++aPtvnsYkRlv++++lsgatWaPa+i++g nnR
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_30085 259 SDPSGMGLSKLAYHFAAGLLAHGPALCAFAAPTVNSYKRLVVGNSLSGATWAPAFIAFGANNR 321
                                                     *************************************************************** PP

                                       TIGR03105 317 thmvRiPdagRlelRlaDgaanpYlvsaavlaaGLdGierkldpgkrkdenlya...eelaek 376
                                                     ++mvR+P +gRle+Rl+D+++npYlvsaa++aaGLdGi+r+l+  + ++enly+   e++a++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_30085 322 SAMVRVP-YGRLEFRLPDAGCNPYLVSAAIIAAGLDGIDRQLEIDHVCNENLYSlslEQIAAR 383
                                                     *******.***********************************************9******* PP

                                       TIGR03105 377 gvetLPqtLlealraleadelleealGkelveeflklkreeweeyhrtvsdWeidryl 434
                                                     g++tLPq+L+ea +alead+l++e lG ++v+ef+klkr+ew+ey+r+vsdWei+ry+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_30085 384 GIKTLPQSLKEACDALEADPLFAEMLGPQIVDEFIKLKRMEWVEYSRHVSDWEIQRYT 441
                                                     ********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (444 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.53
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis